The achlorophyllousholoparasitesLennoa and Pholisma were once regarded as a family, Lennoaceae, but it is now known that they form a clade that is nested within Ehretiaceae.[7] Some studies have indicated that Hydrophyllaceae is paraphyletic if the tribe Nameae is included within it, but further studies will be needed to resolve this issue.[2]

The inclusion of the genus Hoplestigma in Boraginales was occasionally doubted until it was strongly confirmed in a cladistic study in 2014.[1]Hoplestigma is the closest relative of Cordiaceae and it has been recommended that the latter be expanded to include it.

Hydrolea was thought to belong in Hydrophyllaceae for more than a century after it was placed there by Asa Gray, but it is now known to belong in the order Solanales as sister to Sphenoclea.[2]